c5646cd96ffba1bf1574d26abaaa35cd021c448f jnavarr5 Thu Jan 7 14:56:07 2021 -0800 Centering the photos on the page. Using the new image name for the early browser group photo, refs #20314 diff --git src/hg/htdocs/goldenPath/history.html src/hg/htdocs/goldenPath/history.html index ca4d729..0f8659d 100755 --- src/hg/htdocs/goldenPath/history.html +++ src/hg/htdocs/goldenPath/history.html @@ -127,44 +127,44 @@ dominant gene-finding methodology and was used successfully on the <i>Drosophila melanogaster</i> (fruit fly) genome. But the process requires intact long-range genomic sequence to find the genes and the human genome sequence was in many small pieces.</p> <p> At the time UCSC entered the International Human Genome Project (IHGP), the IHGP was assembling the sequence one piece (or, in the jargon of molecular biology, one "clone") at a time, and intended to string the pieces together based on a precisely constructed clone map. This approach had been shown to work very well with <i>Caenorhabditis elegans</i> (a roundworm) and human chromosome 22. But the process of making sure every last part of the sequence is read and put together properly is quite labor-intensive.</p> <p> Haussler enlisted Jim Kent, then a graduate student at UCSC's Department of Molecular, Cell, & Developmental Biology, along with systems engineer Patrick Gavin, and graduate students Terrence Furey and David Kulp (who had led the gene-finding effort on the Drosophila genome). This was the birth of the UCSC Genome Browser group.</p> -<div class="row"> +<div class="row" style="text-align:center"> <div class="col-md-6"> <img class="text-center" alt="Jim next to his computer" src="/images/jim-in-garage.jpg" style="margin-botton:5px; width:500px"> <div style="text-align:center; line-height:1"> <font SIZE=-1> - Jim in his garage sitting next to the computer where he wrote the 10,000 lines of computer - code to assemble the first draft assembly of the human genome. + Jim Kent in his garage sitting next to the computer where he wrote the 10,000 lines of + computer code to assemble the first draft assembly of the human genome. </font> </div> </div> <div class="col-md-6"> - <img class="text-center" alt="Jim, David, Scot, Patrick, and Gavin at UCSC." - src="/images/Jim-Kent-David-Haussler-Scot-Kennedy-Patrick-Gavin-genome-assembly-era-Group-2000.jpg" + <img class="text-center" alt="Jim, David, Patrick, and Scot at UCSC." + src="/images/Jim-Kent-David-Haussler-Patrick-Gavin-Scot-Kennedy-genome-assembly-era-Group-2000.jpg" style="margin-botton:5px; width:400px"> <div style="text-align:center; line-height:1"> <font SIZE=-1> Jim Kent, David Haussler, Parick Gavin and Scot Free Kennedy at UCSC. </font> </div> </div> </div> <a name="celera"></a> <h3>New challenger, Celera Genomics</h3> <p> It was a crucial time for the international project. A private company, <a target="_blank" href="https://en.wikipedia.org/wiki/Celera_Corporation">Celera Genomics</a>, had announced its @@ -206,31 +206,31 @@ <p> In May of 2000, motivated to prevent Celera and its clients from locking up significant portions of the human genome in patents, Jim Kent dropped his other work to focus on the assembly problem. In a remarkable display of energy and talent, Kent developed within four weeks a 10,000-line computer program that assembled the working draft of the human genome. The program, called GigAssembler, constructed the first working draft of the human genome on June 22, 2000, just days before Celera completed its first assembly. The IHGP working draft combined anonymous genomic information from human volunteers of diverse backgrounds, accepted on a first-come, first-taken basis. The Celera sequence was of a single individual. Since the public consortium finished the genome ahead of the private company, the genome and the information it contains are available free to researchers worldwide. Kent's assembly was celebrated at a White House ceremony on June 26, 2000, announcing the completion of the first drafts of the human genome by the IHGP and Celera.</p> </div> - <div class="col-md-6"> + <div class="col-md-6" style="text-align:center"> <img class="text-center" alt="Copy of first draft of the human genome on a CD" src="/images/genome_cd.jpg" style="margin-botton:5px; width:400px"> <div style="text-align:center; line-height:1"> <font SIZE=-1> Copy of first draft of the human genome sequence presented to <a href="https://www.soe.ucsc.edu/news/article/1020" target="_blank">President Clinton</a> and deposited in the Smithsonian. </font> </div> </div> </div> <div class="row"> <div class="col-md-6"> @@ -258,34 +258,34 @@ <p> The UCSC team was a key part of the Hard Core Analysis Group that published in the Feb 15, 2001 issue of Nature. We linked the genome sequence to previous genetic, cytogenetic, and radiation hybrid maps, and to the new physical clone map. We did this both to refine and validate the sequence assembly, and to explore phenomena such as positional and gender variation in recombination rate, regional isochore structure and repeat structure at the single base resolution for the first time. David Kulp performed the mapping of STS markers, messenger RNAs and ESTs, Terry Furey mapped the chromosome band positions, cytogenetic markers (~8,000 gene regions mapped by Fluorescence In-Situ Hybridization) and isochores, and integrated these data with the radiation hybrid and genetic maps. </p> </div> - <div class="col-md-6"> + <div class="col-md-6" style="text-align:center"> <img class="text-center" alt="David in front of Dell cluster" src="/images/david_cluster.jpg" - style="margin-botton:5px; width:400px"> + style="margin-botton:5px; width:350px"> <div style="text-align:center; line-height:1"> <font SIZE=-1> David Haussler next to the original Dell computer cluster used for the assembly of the first human genome. </font> </div> </div> <div class="col-md-12"> <p> The genome sequence at the time of release, however, was simply a few billion characters of Gs, As, Ts and Cs, many of them assigned to chromsomes. As indicated above, however, without landmarks it is unintelligible. During this time, Kent was also working on a computer program that would allow him to view genes of <em>C. elegans</em> and show via a web interface which parts of the genes @@ -356,31 +356,31 @@ Jim Kent with technical management by Kate Rosenbloom, provided the database and web interface for all sequence-related data to the ENCODE project. This included integrating the data into the UCSC Human Genome Browser (where it continues to reside) on specialized tracks, and providing further in-depth information on detail pages. UC Santa Cruz also developed, performed, and presented computational and comparative analyses to glean further genomic and functional information from the collective data.</p> <p> UC Santa Cruz worked closely with labs producing data for the ENCODE project and with data analysis groups to define data and metadata reporting standards for a broad range of genomic assays. They implemented data submission and validation pipelines, created and maintained the <a href="https://www.encodeproject.org/" target="_blank">encodeproject.org</a> website, developed user access tools for ENCODE data, exported all ENCODE data to repositories at the National Center for Biotechnology Information (NCBI), and provided outreach and tutorial support for the project. </p> </div> - <div class="col-md-6"> + <div class="col-md-6" style="text-align:center"> <img class="text-center" alt="Picture of Kate Rosenbloom from 2003" src="/images/kate2003.jpg" style="margin-botton:5px; width:250px"> <div style="text-align:center; line-height:1"> <font SIZE=-1> <p class="gbsCaption text-center"> Kate Rosenbloom while working on the ENCODE Project (2003).</p> </font> </div> </div> </div> <p> The ENCODE data coordination was passed on to the Michael Cherry laboratory at Stanford University in late 2012. UC Santa Cruz, however, continues to support existing ENCODE data and resources on the UCSC Genome Browser website. Researchers can still select ENCODE from the portal at Stanford and